Applied Biosystems provided the oligonucleotides designed by Dr. Brownstein. CIDR staff performed all of the laboratory work related to this project including testing of all primer pairs designed by Dr. Brownstein and genotyping of 54 mouse strains.

View markers for chromosome [all] 1 2 3 4 5 6 7 8 9 10 11 12, 13 14 15, 16 17, 18, 19 X

Data Files and Interactive Queries

A detailed description of this marker set can be found in Witmer et al. 2003: The development of a highly informative mouse simple sequence length polymorphism (SSLP) marker set and construction of a mouse family tree using parsimony analysis. Genome Res 13:485-491.

Dr. Michael Brownstein selected highly informative markers and designed primer sequences which would allow multiplex loading of gels. The initial set of markers developed was designed to be maximally informative for the cross C57BL/6J x DBA/2J. Additional markers were then selected to increase the density of the set and to increase informativeness for other crosses. The forward primer of each pair was labeled on the 5' end with the fluorescent dyes FAM, VIC or NED. All reverse primers were "pig-tailed" with the sequence GTGTCTT (5'-3') to promote addition of +A to the PCR products. Following initial testing, several primer pairs were redesigned to improve performance.

Few if any of the allele sizes using the CIDR primer set will be the same as those observed using the MIT primers. However, the markers will still remain informative using either primer set. The primer sequences are proprietary; the primer set is available for purchase from Applied Biosystems.